This blog is meant to allow Fragment-based Drug Design Practitioners to get together and discuss NON-CONFIDENTIAL issues regarding fragments.

12 June 2017

Fourth NovAliX Biophysics in Drug Discovery Conference

NovAliX held its fourth Biophysics in Drug Discovery meeting last week in the beautiful city of
Strasbourg. This was my first time attending, and although Teddy’s recounting
of the first meeting (here, here and here) had given me high expectations they
were easily exceeded. With 134 participants from 13 countries, most of whom
stayed for the full time, the event felt like a Gordon Research Conference,
with lots of lively discussions over excellent food and drink. Rather than
trying to summarize all 30+ talks and nearly as many posters, I’ll just provide
a few impressions. Conference Chairman Jean-Paul Renaud posted a 2 minute video
overview here.

Factors that drive success in
FBLD were a theme of Jenny Sandmark (AstraZeneca). She discussed several
projects in which fragments were able to generate useful chemical matter, including
one (Complement Factor B) where HTS and DNA-encoded libraries both came up
short. In the case of neutrophil elastase, SAR on HTS hits was making rapid
progress, but chemistry to explore the S1 pocket was difficult. A directed NMR
screen of 800 fragments did not yield anything better, but it did save
considerable synthetic effort and was thus judged a success.

Tweaking experimental conditions
was often essential to get informative results: soaking crystals of
neutrophil elastase with fragments dissolved in DMSO produced no hits, while dissolving the
fragments in water did. With crystals of Factor XIa, glycerol – not fragments –
bound in the active site. Fortunately the researchers recognized this and were
able to use a different cryoprotectant.

Glyn Williams (Astex) has been
doing FBLD since the earliest days, and discussed some of the lessons learned. Although
the current Astex fragment library consists of about 1800 compounds, some 8000
fragments have been evaluated over the years. Small fragments in particular can
be quite volatile, so Astex stores its library at -80 °C under nitrogen. Researchers
also do rigorous quality control (QC) and maintain “fragment CVs”, which
summarize analytical and screening data for each molecule. Astex is heavily
invested in synthesizing novel fragments to explore specific regions of chemical
space, and this means being constantly on guard for risks such as redox cyclers.

Understanding the enemy is always
useful, so Martin Redhead (UCB) has constructed a library of bad actors –
including PAINS, chelators, and metals – to stress-test his assays. But even robust assays show plenty of false positives. A screen of
20,000 molecules against a protein-protein interaction revealed 105
stabilizers, only 3 of which turned out to be real, but four times as many
inhibitors, none of which were legitimate.
Some of the stabilizers could subsequently be modified to inhibitors,
and Martin suggested that screening for stabilizers initially could be a
general way of improving signal to noise.

NMR is uniquely capable of
providing extensive QC information about both proteins and ligands, and Alvar
Gossert (ETH) discussed how a “validation cross” confirming both integrity and
binding can improve confidence. Alvar also discussed using dynamic nuclear
polarization to reduce the number of spectra required to assign a protein from
five collected over two weeks to one obtained in under three days. This
requires a specialized setup involving a second magnet, but it does appear powerful.
Another unusual NMR configuration was described by Ad Bax (NIH), who is studying
protein folding by rapidly (< 1 msec) increasing the pressure of a sample to
2500 bar – the equivalent energy of “discharging a small handgun into your NMR.”

Plenty of more accessible
technologies were also described, including some interesting new commercial
offerings. Matyas Vegh (Creoptix) discussed using waveguide interferometry to
study protein-ligand interactions. This is similar to surface plasmon resonance
(SPR) but with higher sensitivity and lower bulk effect. Their new four-channel
instrument can be temperature controlled from 4-45 °C and is capable of
accurately measuring kinetics even for weak binders, such as the 2.79 s-1
off-rate for the binding of methylsulfonamide (MW = 95 Da, Kd = 419 µM)
to carbonic anhydrase II. And Sven Malik (Sierra Sensors) described a sensitive
new SPR instrument with 8 channels, each with 4 spots, capable of running 384
samples in under 3 hours.

Several talks or posters highlighted
an instrument from Biodesy which is capable of studying sub-Ångström conformational
changes in dye-labeled, surface-immobilized proteins using second harmonic
generation. Their plate-based instrument can measure 20,000 samples per week.
Elizabeth Vo (UCSF) is using this to study the protein K-Ras, and has identified
a number of active fragments which are being further characterized using
orthogonal methods. It will be fun to see how these compare with previously
reported K-Ras binders.

Finally, the keynote lecture was
delivered by Jean-Pierre Changeux (Collège de France and Institut Pasteur), who
described some of the highlights – many of them quite recent – from a career
that spans nearly six decades. Jean-Pierre literally invented the model for
allostery at a time when the three dimensional structures of only two proteins
were known; today the Protein Data Bank contains more than 130,000 structures,
and at least 90 marketed drugs are known to work through allosteric
mechanisms. It is humbling to be reminded of how far we've come, yet
how little we still know.

Strasbourg is a wonderful city,
but with today’s travel budgets it can be difficult to access for some
researchers, so next year the conference will head to Boston (June 12-15), returning to Strasbourg in 2019 before moving on to Kyoto
in 2020. Hope to see you there!